Unraveling genetic diversity and selection signatures in rice: insights from whole-genome resequencing for precision breeding

Rice breeding faces numerous challenges in selecting potential materials that combine high grain yield with enhanced adaptability to diverse conditions and stress-prone environments. We sequenced the genomes of 70 conventional japonica rice varieties from Zhejiang Province to assess their genetic diversity and provide genomic support for future rice breeding efforts. Whole-genome resequencing technology serves as an effective tool for elucidating genetic diversity, deciphering population structure, and exploring adaptive evolution of rice germplasm, providing valuable insights for advancing molecular breeding efforts. To enhance the utilization of japonica genetic resources and facilitate the breeding of new varieties, a study utilizing whole-genome resequencing analysis was performed on genetic data from 70 japonica rice accessions originating in Zhejiang Province, China. We systematically investigated genetic diversity, population structure, and selection signatures through phylogenetic tree construction, principal component analysis (PCA), and select elimination analysis. Our findings revealed that the conventional japonica rice varieties in this region exhibit substantial genetic diversity, with distinct population stratification into two genetically divergent subgroups. Through select elimination analysis, 112 genomic regions that had undergone selection pressure during the breeding process were identified. Subsequent KEGG and GO enrichment analyses of candidate genes within these selected genomic regions provided a foundation for future research on gene function. Additionally, haplotype analysis further revealed significant allelic variations correlated with agronomic traits, providing valuable genetic information for improving rice varieties. This research establishes a robust genomic foundation for precision breeding and provides actionable insights to optimize the development of improved japonica rice varieties. Our findings reveal two genetically distinct subgroups among Zhejiang japonica rice varieties, with different levels of diversity reflecting their breeding histories. We identified multiple genomic regions and candidate genes that likely experienced selection. These results provide a genomic basis for more targeted use of Zhejiang japonica germplasm in future breeding efforts.